AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00580_mtub_reg_300.orf -o00580_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 glpQ2 300 glpQ2 #2 Rv3843c 300 hypothetical protein Rv3843c Motif number 1 GTTCGATTCCCGTCATCGGCTCCGATGTGA 1 30 1 CGTCATCGGC 0.88755 -271 CGATGTGACACGTCGACGCTGATGGTGATG 1 52 1 CGTCGACGCT 0.947209 -249 TGATGCTGAACGTCGGTGGCCCGGCGGCAA 1 77 1 CGTCGGTGGC 0.981356 -224 GCCTTCCCCGCCTTGCCGCCGGGCCACCGA 1 89 0 CCTTGCCGCC 0.72464 -212 GGCGGCAAGGCGGGGAAGGCCCAAAACGAT 1 99 1 CGGGGAAGGC 0.915329 -202 AAACGATGGCCGGCCCATGCACCGTCGTCG 1 122 1 CGGCCCATGC 0.807128 -179 GCGCGGTCGGCGACGACGGTGCATGGGCCG 1 132 0 CGACGACGGT 0.941696 -169 CCGTCGTCGCCGACCGCGCCGTATGGGAGC 1 143 1 CGACCGCGCC 0.993168 -158 CCGCGCCGTATGGGAGCGCCCATTACCACT 1 156 1 TGGGAGCGCC 0.93405 -145 CGCTTTCGCATCGCAGTGGTAATGGGCGCT 1 170 0 TCGCAGTGGT 0.543926 -131 CACTGCGATGCGAAAGCGGCTGGTGCACAG 1 182 1 CGAAAGCGGC 0.91206 -119 ACCGCTCTGTCGGCGACGGTTCCTGTGCAC 1 204 0 CGGCGACGGT 0.98217 -97 GCCGACAGAGCGGTGCTGCCCCCGGCGTGG 1 220 1 CGGTGCTGCC 0.824099 -81 CCGCCGGGGGCGTCCACGCCGGGGGCAGCA 1 233 0 CGTCCACGCC 0.984348 -68 ACGCCCCCGGCGGCCGAGGCTATGTGATAC 1 250 1 CGGCCGAGGC 0.992043 -51 ACCTGATGAGCGACGGTGGCGCACCTACC 1 282 1 CGACGGTGGC 0.972733 -19 CGCTCGGGTACCTGCCAGGCTGTCGATGAG 2 27 1 CCTGCCAGGC 0.778893 -274 AACGCATTGACGGGCGCTGTTATCCACAGT 2 57 1 CGGGCGCTGT 0.816608 -244 TCCACAGTTGTGGGCCTGGCTGACGGATGG 2 79 1 TGGGCCTGGC 0.85236 -222 GGCTGACGGATGGAGCCGGTGTTAACGCCA 2 96 1 TGGAGCCGGT 0.705832 -205 ACAGCTTTATCCACAGCGGTAAGAATCCGA 2 130 0 CCACAGCGGT 0.899174 -171 ACGTCCAGCACGACACAGCTACCTACGACT 2 173 0 CGACACAGCT 0.729891 -128 TGTGTCGTGCTGGACGTGCCGCGACCGGGC 2 186 1 TGGACGTGCC 0.696453 -115 GTGCCGCGACCGGGCGCGCCCAATCCAGCG 2 201 1 CGGGCGCGCC 0.994428 -100 TTGAGGCAGGCTTCCGCGCTGGATTGGGCG 2 217 0 CTTCCGCGCT 0.738447 -84 CGGAAGCCTGCCTCAACGCCTGTTGACGGC 2 231 1 CCTCAACGCC 0.893185 -70 GGTACGGCATTGTCCGCGCCGTCAACAGGC 2 248 0 TGTCCGCGCC 0.973947 -53 CTTCTCCGCCCCGCACCGGTACGGCATTGT 2 265 0 CCGCACCGGT 0.949713 -36 ********** Masking position 8 Map Score: 42.1 Number of sites scoring better than the average of aligned sites = 137883 Number in coding regions = 130380 Number in noncoding regions = 7503 Number of orfs with sites within 600 bp upstream = 1723 Fraction of orfs with sites within 600 bp upstream = 0.276743 Motif number 2 CACATCGGAGCCGATGACGGGAATCGAACC 1 29 0 CCGATGACGG 0.755896 -272 CACGTCGACGCTGATGGTGATGCTGAACGT 1 60 1 CTGATGGTGA 0.876014 -241 TCGGCGACGACGGTGCATGGGCCGGCCATC 1 126 0 CGGTGCATGG 0.897662 -175 CCATACGGCGCGGTCGGCGACGACGGTGCA 1 139 0 CGGTCGGCGA 0.960857 -162 GCGACGGTTCCTGTGCACCAGCCGCTTTCG 1 192 0 CTGTGCACCA 0.806888 -109 CAGCACCGCTCTGTCGGCGACGGTTCCTGT 1 208 0 CTGTCGGCGA 0.980363 -93 ACCTGCCAGGCTGTCGATGAGAACGCATTG 2 36 1 CTGTCGATGA 0.984529 -265 AGGCCCACAACTGTGGATAACAGCGCCCGT 2 66 0 CTGTGGATAA 0.968748 -235 ATTCTTACCGCTGTGGATAAAGCTGTGGAA 2 134 1 CTGTGGATAA 0.968748 -167 GCTGTGGAAACTGTGGATAGTCGTAGGTAG 2 155 1 CTGTGGATAG 0.88634 -146 GCCTCAACGCCTGTTGACGGCGCGGACAAT 2 240 1 CTGTTGACGG 0.886378 -61 ********** Masking position 1 Map Score: 14.447 Number of sites scoring better than the average of aligned sites = 3555 Number in coding regions = 3272 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 3 CACATCGGAGCCGATGACGGGAATCGAACCCG 1 27 0 CCGGACGGGA 0.982775 -274 TGCTGAACGTCGGTGGCCCGGCGGCAAGGCGG 1 80 1 CGGGCCCGGC 0.988686 -221 CGGCGGCAAGGCGGGGAAGGCCCAAAACGATG 1 98 1 GCGGAAGGCC 0.827054 -203 AGGCCCAAAACGATGGCCGGCCCATGCACCGT 1 115 1 CGAGCCGGCC 0.986709 -186 CCATGCACCGTCGTCGCCGACCGCGCCGTATG 1 136 1 TCGGCCGACC 0.934039 -165 TGCACAGGAACCGTCGCCGACAGAGCGGTGCT 1 205 1 CCGGCCGACA 0.900722 -96 GCCGGGGGCGTCCACGCCGGGGGCAGCACCGC 1 229 0 TCCGCCGGGG 0.651649 -72 CACATAGCCTCGGCCGCCGGGGGCGTCCACGC 1 244 0 CGGGCCGGGG 0.977231 -57 GCGTTCTCATCGACAGCCTGGCAGGTACCCGA 2 30 0 CGAGCCTGGC 0.979164 -271 CGATGAGAACGCATTGACGGGCGCTGTTATCC 2 50 1 GCAGACGGGC 0.945778 -251 TATCCACAGTTGTGGGCCTGGCTGACGGATGG 2 77 1 TGTGCCTGGC 0.759753 -224 CGGTAAGAATCCGACGAATGGCGTTAACACCG 2 112 0 CCGGAATGGC 0.931915 -189 GCTGGACGTGCCGCGACCGGGCGCGCCCAATC 2 194 1 CCGACCGGGC 0.992685 -107 CAATCCAGCGCGGAAGCCTGCCTCAACGCCTG 2 221 1 CGGGCCTGCC 0.991884 -80 ATTGTCCGCGCCGTCAACAGGCGTTGAGGCAG 2 238 0 CCGAACAGGC 0.7946 -63 CAATGCCGTACCGGTGCGGGGCGGAGAAGTCA 2 266 1 CCGGCGGGGC 0.992439 -35 *** ******* Masking position 6 Map Score: 29.9627 Number of sites scoring better than the average of aligned sites = 24355 Number in coding regions = 22670 Number in noncoding regions = 1685 Number of orfs with sites within 600 bp upstream = 944 Fraction of orfs with sites within 600 bp upstream = 0.151622 Motif number 4 TCCCAAGCTGAATACGCGGGTTCGATT 1 7 1 GCTGAATAGC 0.85679 -294 CGGCGGCAAGGCGGGGAAGGCCCAAAACGAT 1 98 1 GCGGGGAAGC 0.993257 -203 TTACCACTGCGATGCGAAAGCGGCTGGTGCA 1 178 1 GATGCGAAGC 0.961012 -123 AGGAACCGTCGCCGACAGAGCGGTGCTGCCC 1 210 1 GCCGACAGGC 0.950992 -91 GACGCCCCCGGCGGCCGAGGCTATGTGATAC 1 249 1 GCGGCCGAGC 0.97 -52 CCAGGCTGTCGATGAGAACGCATTGACGGGC 2 41 1 GATGAGAAGC 0.977382 -260 TCTTACCGCTGTGGATAAAGCTGTGGAAACT 2 136 1 GTGGATAAGC 0.923926 -165 TGTTGACGGCGCGGACAATGCCGTACCGGTG 2 251 1 GCGGACAAGC 0.997198 -50 CCGGTGCGGGGCGGAGAAGTCACTAGGCTGG 2 276 1 GCGGAGAATC 0.979423 -25 ******** ** Masking position 11 Map Score: 10.8368 Number of sites scoring better than the average of aligned sites = 2909 Number in coding regions = 2746 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 5 GGCCCACAACTGTGGATAACAGCGCCCGTC 2 65 0 TGTGGATAAC 0.991094 -236 TTCTTACCGCTGTGGATAAAGCTGTGGAAA 2 135 1 TGTGGATAAA 0.986841 -166 CTGTGGAAACTGTGGATAGTCGTAGGTAGC 2 156 1 TGTGGATAGT 0.984403 -145 ********** Masking position 6 Map Score: 0.865781 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 5 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0